Briefings in Bioinformatics

Article	Citations
Dynamic changes of synergy relationship between lncRNA and immune checkpoint in cancer progression	1026
Deep learning reveals determinants of transcriptional infidelity at nucleotide resolution in the allopolyploid line by goldfish and common carp hybrids	626
COWID: an efficient cloud-based genomics workflow for scalable identification of SARS-COV-2	610
QOT: Quantized Optimal Transport for sample-level distance matrix in single-cell omics	501
CpGFuse: a holistic approach for accurate identification of methylation states of DNA CpG sites	362
ETLD: an encoder-transformation layer-decoder architecture for protein contact and mutation effects prediction	320
Ensemble classification based feature selection: a case of identification on plant pentatricopeptide repeat proteins	233
Correction to: Addressing barriers in comprehensiveness, accessibility, reusability, interoperability and reproducibility of computational models in systems biology	231
Addressing scalability and managing sparsity and dropout events in single-cell representation identification with ZIGACL	222
Systematic evaluation of de novo mutation calling tools using whole genome sequencing data	196
Stoichiometry-preserving and stochasticity-aware identification of m6A from direct RNA sequencing	180
Assessing protein model quality based on deep graph coupled networks using protein language model	162
Towards comprehensive benchmarking of medical vision language models	154
A novel prognostic framework for HBV-infected hepatocellular carcinoma: insights from ferroptosis and iron metabolism proteomics	151
Improving the performance of single-cell RNA-seq data mining based on relative expression orderings	148
Ensemble learning based on matrix completion improves microbe-disease association prediction	140
MicroHDF: predicting host phenotypes with metagenomic data using a deep forest-based framework	140
Genome assembly and gene identification of biosurfactant-producing bacteria for environmental bioremediation	129
Computational refinement and multivalent engineering of complementarity-determining region-grafted nanobodies on a humanized scaffold for retaining antiviral efficacy	128
Building multiscale models with PhysiBoSS, an agent-based modeling tool	128
Multi-marker testing based on accelerated failure time models under possible left truncation and competing risks	122
Self-supervised learning with chemistry-aware fragmentation for effective molecular property prediction	122
Cox-Sage: enhancing Cox proportional hazards model with interpretable graph neural networks for cancer prognosis	116
IGCNSDA: unraveling disease-associated snoRNAs with an interpretable graph convolutional network	115
scAnno: a deconvolution strategy-based automatic cell type annotation tool for single-cell RNA-sequencing data sets	115

Inferring disease-associated circRNAs by multi-source aggregation based on heterogeneous graph neural network	114
GeNePi: a graphics processing unit enhanced next-generation bioinformatics pipeline for whole-genome sequencing analysis	113
Blood-based transcriptomic signature panel identification for cancer diagnosis: benchmarking of feature extraction methods	110
mbDecoda: a debiased approach to compositional data analysis for microbiome surveys	103
CLT-seq as a universal homopolymer-sequencing concept reveals poly(A)-tail-tuned ncRNA regulation	103
BayesKAT: bayesian optimal kernel-based test for genetic association studies reveals joint genetic effects in complex diseases	101
PRIEST: predicting viral mutations with immune escape capability of SARS-CoV-2 using temporal evolutionary information	100
A robust statistical approach for finding informative spatially associated pathways	99
STEAM: Spatial Transcriptomics Evaluation Algorithm and Metric for clustering performance	98
Multi-modal domain adaptation for revealing spatial functional landscape from spatially resolved transcriptomics	98
Clustered tree regression to learn protein energy change with mutated amino acid	95
DADA-EV: domain-adaptive diffusion autoencoder for estimating tissue- and cell-type-specific origin in extracellular vesicle transcriptomes	93
Learning discriminative and structural samples for rare cell types with deep generative model	93
Protein phosphorylation database and prediction tools	93
Hi-C3: a statistical inference-based model for reconstructing higher-order cell–cell communication networks	93
Nonlinear kernel-based high-dimensional inference for set-based genetic association studies	92
Novel multi-omics deconfounding variational autoencoders can obtain meaningful disease subtyping	91
Integrating AlphaFold and deep learning for atomistic interpretation of cryo-EM maps	91
Melanoma 2.0. Skin cancer as a paradigm for emerging diagnostic technologies, computational modelling and artificial intelligence	89
Making PBPK models more reproducible in practice	87
PMiSLocMF: predicting miRNA subcellular localizations by incorporating multi-source features of miRNAs	86
Computational model for ncRNA research	84
Clustering scRNA-seq data with the cross-view collaborative information fusion strategy	84
AICellType: a large language model-based platform for accurate cell type annotation	82
DeepCheck: multitask learning aids in assessing microbial genome quality	81
Analysis of super-enhancer using machine learning and its application to medical biology	80
A chronotherapeutics-applicable multi-target therapeutics based on AI: Example of therapeutic hypothermia	79
scGAD: a new task and end-to-end framework for generalized cell type annotation and discovery	79
Identification of vital chemical information via visualization of graph neural networks	79
Improving drug response prediction via integrating gene relationships with deep learning	79
A comprehensive benchmark of tools for efficient genomic interval querying	78
ULDNA: integrating unsupervised multi-source language models with LSTM-attention network for high-accuracy protein–DNA binding site prediction	78
DriverOmicsNet: an integrated graph convolutional network for multi-omics exploration of cancer driver genes	77
Beyond metaphor: quantitative reconstruction of Waddington landscape and exploration of cellular behavior	77
GAABind: a geometry-aware attention-based network for accurate protein–ligand binding pose and binding affinity prediction	76
HighFold: accurately predicting structures of cyclic peptides and complexes with head-to-tail and disulfide bridge constraints	74
Graph-based RNA structural representation reveals determinants of subcellular localization	74
Predicting microbe–drug associations with structure-enhanced contrastive learning and self-paced negative sampling strategy	73
Attribute-guided prototype network for few-shot molecular property prediction	73
FGeneBERT: function-driven pre-trained gene language model for metagenomics	72
Subtype-DCC: decoupled contrastive clustering method for cancer subtype identification based on multi-omics data	72
Machine learning modeling of RNA structures: methods, challenges and future perspectives	72
Large-scale predicting protein functions through heterogeneous feature fusion	70
Machine learning–augmented m6A-Seq analysis without a reference genome	68
A multichannel graph neural network based on multisimilarity modality hypergraph contrastive learning for predicting unknown types of cancer biomarkers	68
Protein–DNA binding sites prediction based on pre-trained protein language model and contrastive learning	67
AptaDiff: de novo design and optimization of aptamers based on diffusion models	67
IRCAS: a novel end-to-end approach to identify, rectify, and classify comprehensive alternative splicing events in a transcriptome without genome reference	67
QTFPred: robust high-performance quantum machine learning modeling that predicts main and cooperative transcription factor bindings with base resolution	66
Evaluating large language models for annotating proteins	66

Clover: tree structure-based efficient DNA clustering for DNA-based data storage	65
Multiple errors correction for position-limited DNA sequences with GC balance and no homopolymer for DNA-based data storage	65
Detecting tipping points of complex diseases by network information entropy	64
PLMFit: benchmarking transfer learning with protein language models for protein engineering	64
Directed evolution of antimicrobial peptides using multi-objective zeroth-order optimization	64
dHICA: a deep transformer-based model enables accurate histone imputation from chromatin accessibility	63
An overview of self-supervised deep learning applications to molecular data	63
Graph-RPI: predicting RNA–protein interactions via graph autoencoder and self-supervised learning strategies	63
cfMethylPre: deep transfer learning enhances cancer detection based on circulating cell-free DNA methylation profiling	63
Predicting protein–carbohydrate binding sites: a deep learning approach integrating protein language model embeddings and structural features	63
A social theory-enhanced graph representation learning framework for multitask prediction of drug–drug interactions	63
Ligand-agnostic off-target site prediction for early toxicity screening by leveraging point cloud-based protein cavity analysis	62
Benchmarking of computational methods for m6A profiling with Nanopore direct RNA sequencing	62
Phage quest: a beginner’s guide to explore viral diversity in the prokaryotic world	62
SCSMD: Single Cell Consistent Clustering based on Spectral Matrix Decomposition	62
Correction to: Computational toxicology in drug discovery: applications of artificial intelligence in ADMET and toxicity prediction	61
Correction to: sciCNV: high-throughput paired profiling of transcriptomes and DNA copy number variations at single-cell resolution	61
Deep learning in integrating spatial transcriptomics with other modalities	61
SAMURAI: shallow analysis of copy number alterations using a reproducible and integrated bioinformatics pipeline	61
TransIntegrator: capture nearly full protein-coding transcript variants via integrating Illumina and PacBio transcriptomes	61
From intuition to AI: evolution of small molecule representations in drug discovery	61
Systematic investigation of the homology sequences around the human fusion gene breakpoints in pan-cancer – bioinformatics study for a potential link to MMEJ	61
Deciphering gene contributions and etiologies of somatic mutational signatures of cancer	61
AI-assisted patient matching for personalized cancer medicine	60
Multilevel superposition for deciphering the conformational variability of protein ensembles	59
A novel approach to study multi-domain motions in JAK1’s activation mechanism based on energy landscape	59
slORFfinder: a tool to detect open reading frames resulting from trans-splicing of spliced leader sequences	59
Clinical and data-driven optimization of Genomiser for rare disease patients: experience from the Hong Kong Genome Project	58
Improving multi-population genomic prediction accuracy using multi-trait GBLUP models which incorporate global or local genetic correlation information	58
Knowledge-guided multi-level network modeling with experimental characterization identifies PRKCA as a novel biomarker and tumor suppressor triggering ferroptosis in prostate cancer	58
Nativeness-constrained diffusion framework for nanobody design	58
Therapeutic peptides identification via kernel risk sensitive loss-based k-nearest neighbor model and multi-Laplacian regularization	58
Robust discovery of gene regulatory networks from single-cell gene expression data by Causal Inference Using Composition of Transactions	57
OmniDoublet: a method for doublet detection in multimodal single-cell sequencing data	57
scAED: a framework for mapping the enhancer state at single-cell resolution	57
A novel computational model ITHCS for enhanced prognostic risk stratification in ESCC by correcting for intratumor heterogeneity	57
CHAI: consensus clustering through similarity matrix integration for cell-type identification	57
A risk assessment framework for multidrug-resistant Staphylococcus aureus using machine learning and mass spectrometry technology	57
ceQTL: a co-expression QTL model to detect a variant that affects transcription factor binding and its target regulation	56
Reconstructing 3D transcriptional organization from spatial transcriptomics reveals consistent oncogenic translocations and developmental dynamics	56
Estimating population structure using epigenome-wide methylation data	55
Component puzzle protein–protein interaction prediction	55
Quantifying transcript complexity via the condition number of gene-specific random matrix	54
Metatranscriptomic analysis uncovers microbial and immune signatures underlying COVID-19 severity	54
Comprehensive machine learning boosts structure-based virtual screening for PARP1 inhibitors	53
MSF-CPMP: a novel multi-source feature fusion model for prediction of cyclic peptide membrane permeability	53
PGVDA: a pathway-aggregated genetic dosage framework for interpretable disease classification using machine learning	53
Enhancing protein structure prediction: evaluating the role of amino acid physicochemical features in homology search	53
The improved de Bruijn graph for multitask learning: predicting functions, subcellular localization, and interactions of noncoding RNAs	52
Phylogenetic inference of inter-population transmission rates for infectious diseases	52
Denoising adaptive deep clustering with self-attention mechanism on single-cell sequencing data	52
TaxaGO: a novel, phylogenetically informed gene ontology enrichment analysis tool	52
SGCLDGA: unveiling drug–gene associations through simple graph contrastive learning	51
BioWorkflow: Retrieving comprehensive bioinformatics workflows from publications	51
Quantum ensembling methods for healthcare and life science	51
PredLLPS_PSSM: a novel predictor for liquid–liquid protein separation identification based on evolutionary information and a deep neural network	50
ReCIDE: robust estimation of cell type proportions by integrating single-reference-based deconvolutions	50
A review of methods for predicting DNA N6-methyladenine sites	50
Robustness and resilience of computational deconvolution methods for bulk RNA sequencing data	50
AnnoAgent: a language agent for single-cell automatic annotation	50
A transformer-based deep learning survival prediction model and an explainable XGBoost anti-PD-1/PD-L1 outcome prediction model based on the cGAS-STING-centered pathways in hepatocellular carcinoma	50
A novel heterophilic graph diffusion convolutional network for identifying cancer driver genes	50
scAMAC: self-supervised clustering of scRNA-seq data based on adaptive multi-scale autoencoder	50
SPNE: sample-perturbed network entropy for revealing critical states of complex biological systems	49
Seq2Topt: a sequence-based deep learning predictor of enzyme optimal temperature	49
Concepts and methods for transcriptome-wide prediction of chemical messenger RNA modifications with machine learning	49
Complexity of enhancer networks predicts cell identity and disease genes revealed by single-cell multi-omics analysis	49
A comprehensive computational benchmark for evaluating deep learning-based protein function prediction approaches	49
Toward high-efficiency, low-resource, and explainable neuropeptide prediction with MSKDNP	48
Efficient prediction of peptide self-assembly through sequential and graphical encoding	48
Interpretable high-order knowledge graph neural network for predicting synthetic lethality in human cancers	48
ncRNAInter: a novel strategy based on graph neural network to discover interactions between lncRNA and miRNA	48
TCM-navigator, a deep learning-based workflow for generation and evaluation of traditional Chinese medicine-like compounds for drug development	48
Integrated multimodal hierarchical fusion and meta-learning for enhanced molecular property prediction	48
scDeepInsight: a supervised cell-type identification method for scRNA-seq data with deep learning	48
FactVAE: a factorized variational autoencoder for single-cell multi-omics data integration analysis	48
Structure-enhanced deep learning accelerates aptamer selection for small molecule families like steroids	47
Advancing microbial diagnostics: a universal phylogeny guided computational algorithm to find unique sequences for precise microorganism detection	47
Data-driven selection of analysis decisions in single-cell RNA-seq trajectory inference	47
Revealing the antimicrobial potential of traditional Chinese medicine through text mining and molecular computation	47

Estimation of non-equilibrium transition rate from gene expression data	47
HLAIImaster: a deep learning method with adaptive domain knowledge predicts HLA II neoepitope immunogenic responses	47
A comprehensive benchmarking of differential splicing tools for RNA-seq analysis at the event level	46
Predicting molecular properties based on the interpretable graph neural network with multistep focus mechanism	46
Comparative epigenome analysis using Infinium DNA methylation BeadChips	46
IEPAPI: a method for immune epitope prediction by incorporating antigen presentation and immunogenicity	46
Multi-omics regulatory network inference in the presence of missing data	46
SPANN: annotating single-cell resolution spatial transcriptome data with scRNA-seq data	46
Inferring kinase–phosphosite regulation from phosphoproteome-enriched cancer multi-omics datasets	45
Paradigms, innovations, and biological applications of RNA velocity: a comprehensive review	45
Development and validation of an explainable machine learning model for predicting multidimensional frailty in hospitalized patients with cirrhosis	45
dSCOPE: a software to detect sequences critical for liquid–liquid phase separation	44
Towards accurate artificial intelligence models for strain-level phage–host prediction	44
AI-guided discovery and optimization of antimicrobial peptides through species-aware language model	44
Drug repositioning based on weighted local information augmented graph neural network	44
scEWE: high-order element-wise weighted ensemble clustering for heterogeneity analysis of single-cell RNA-sequencing data	44
Beyond static structures: protein dynamic conformations modeling in the post-AlphaFold era	43
Cross-modality representation and multi-sample integration of spatially resolved omics data	43
Learning genotype–phenotype associations from gaps in multi-species sequence alignments	43
Bioinformatics toolbox for exploring target mutation-induced drug resistance	43
EDS-Kcr: deep supervision based on large language model for identifying protein lysine crotonylation sites across multiple species	43
Inferring single-cell resolution spatial gene expression via fusing spot-based spatial transcriptomics, location, and histology using GCN	43
MulNet: a scalable framework for reconstructing intra- and intercellular signaling networks from bulk and single-cell RNA-seq data	43
Predictive modelling of acute Promyelocytic leukaemia resistance to retinoic acid therapy	43
Mapping cancer heterogeneity: a consensus network approach to subtypes and pathways	43
iEnhance: a multi-scale spatial projection encoding network for enhancing chromatin interaction data resolution	43
Deep learning in structural bioinformatics: current applications and future perspectives	43
Forecasting dominance of SARS-CoV-2 lineages by anomaly detection using deep AutoEncoders	43
Correction to: Diagnostic Prediction of portal vein thrombosis in chronic cirrhosis patients using data-driven precision medicine model	43
MetaGeno: a chromosome-wise multi-task genomic framework for ischaemic stroke risk prediction	42
A comprehensive benchmark study of methods for identifying significantly perturbed subnetworks in cancer	42
Current computational tools for protein lysine acylation site prediction	42
Machine learning-assisted substrate binding pocket engineering based on structural information	42
PepTCR-Net: prediction of multi-class antigen peptides by T-cell receptor sequences with deep learning	42
D3EGFR: a webserver for deep learning-guided drug sensitivity prediction and drug response information retrieval for EGFR mutation-driven lung cancer	42
HHOMR: a hybrid high-order moment residual model for miRNA-disease association prediction	41
Whole-genome bisulfite sequencing data analysis learning module on Google Cloud Platform	41
GiGs: graph-based integrated Gaussian kernel similarity for virus–drug association prediction	41
Single-cell mosaic integration and cell state transfer with auto-scaling self-attention mechanism	41
Adjustment of scRNA-seq data to improve cell-type decomposition of spatial transcriptomics	40
Could statistical potential models achieve comparable or better performance than deep learning models?	40
scEGG: an exogenous gene-guided clustering method for single-cell transcriptomic data	40
Predictive multispecies constraint-based metabolic modeling: case studies and best practices	40
CosGeneGate selects multi-functional and credible biomarkers for single-cell analysis	40
CELLetter: leveraging large language model and dual-stream network to identify context-specific ligand–receptor interactions for cell–cell communication analysis	40
Identification of molecular subtypes of dementia by using blood-proteins interaction-aware graph propagational network	40
Incremental modelling and analysis of biological systems with fuzzy hybrid Petri nets	40
Cross-RNA transferable sequence representation learning for lncRNA m6A site detection via novel deep domain separation networks	39
Matrix reconstruction with reliable neighbors for predicting potential MiRNA–disease associations	39
Interpretable artificial intelligence model for accurate identification of medical conditions using immune repertoire	39
Integrative analysis of multi-omics and imaging data with incorporation of biological information via structural Bayesian factor analysis	39
Disrupting explicit encoding paradigms: property-interactive transformers decode T-cell receptor specificity beyond dataset biases	39
An automatic immunofluorescence pattern classification framework for HEp-2 image based on supervised learning	39
ComABAN: refining molecular representation with the graph attention mechanism to accelerate drug discovery	39
DRdriver: identifying drug resistance driver genes using individual-specific gene regulatory network	39
Microbe-bridged disease-metabolite associations identification by heterogeneous graph fusion	39
Towards Comprehensive Benchmarking of Medical Vision Language Models	38
Advancing single-cell RNA-seq data analysis through the fusion of multi-layer perceptron and graph neural network	38
Causal Temporal Diffusion Networks for Drug Repurposing in Epilepsy	38
Uncovering allosteric communication in cancer-related histone mutations	38
Learning single-cell chromatin accessibility profiles using meta-analytic marker genes	38
Combining evolution and protein language models for an interpretable cancer driver mutation prediction with D2Deep	38
Evaluation of single-cell RNAseq labelling algorithms using cancer datasets	38
PPRS-ID: Indonesian-adjusted partitioned PRS for type 2 diabetes using obesity PRS integration and west Javanese population LD mapping	38
Master of Metals2: a graph neural network based architecture for the prediction of zinc binding sites in protein structures	38
Predicting differentially methylated cytosines in TET and DNMT3 knockout mutants via a large language model	38
Few-shot drug synergy prediction via rapid cross-tier adaptation meta-optimization	38
Advancing edge-based clustering and graph embedding for biological network analysis: a case study in RASopathies	38
SAM-DTA: a sequence-agnostic model for drug–target binding affinity prediction	38
CACIMAR: cross-species analysis of cell identities, markers, regulations, and interactions using single-cell RNA sequencing data	38
The landscape of the methodology in drug repurposing using human genomic data: a systematic review	37
scHILL: deciphering individual-level immune cell heterogeneity with single-cell RNA sequencing data	37
MGEGFP: a multi-view graph embedding method for gene function prediction based on adaptive estimation with GCN	37
MAK: a machine learning framework improved genomic prediction via multi-target ensemble regressor chains and automatic selection of assistant traits	37
BloodNet: An attention-based deep network for accurate, efficient, and costless bloodstain time since deposition inference	37
Optimized phenotyping of complex morphological traits: enhancing discovery of common and rare genetic variants	36
Identify potential drug candidates within a high-quality compound search space	36
Toward next-generation machine learning and deep learning for spatial omics	36
Benchmarking genome assembly methods on metagenomic sequencing data	36
A kinetic model for solving a combination optimization problem in ab-initio Cryo-EM 3D reconstruction	36
Data-driven patient stratification of UK Biobank cohort suggests five endotypes of multimorbidity	36
GSTRPCA: irregular tensor singular value decomposition for single-cell multi-omics data clustering	36
Deciphering hierarchical regulatory network of cell fate via an epigenetics-informed heterogeneous graph transformer on single-cell multi-omics data	36
graphB3—an interpretable graph learning approach for predicting blood–brain barrier permeability	36
MegSite: an accurate nucleic acid-binding residue prediction method based on multimodal protein language model	35
Spatially contrastive variational autoencoder for deciphering tissue heterogeneity from spatially resolved transcriptomics	35
Current approaches and outstanding challenges of functional annotation of metabolites: a comprehensive review	35
toxCSM: comprehensive prediction of small molecule toxicity profiles	35
GSCA: an integrated platform for gene set cancer analysis at genomic, pharmacogenomic and immunogenomic levels	35
Circling in on plasmids: benchmarking plasmid detection and reconstruction tools for short-read data from diverse species	35
Multi-level multi-view network based on structural contrastive learning for scRNA-seq data clustering	35
Improved prediction of DNA and RNA binding proteins with deep learning models	35
Decoding apoptosis, ferroptosis, and inflammatory cell death in adenomyosis at single-cell resolution	35
A review of biomedical datasets relating to drug discovery: a knowledge graph perspective	35
Prediction of multi-relational drug–gene interaction via Dynamic hyperGraph Contrastive Learning	35